+Open data
-Basic information
Entry | Database: PDB / ID: 5vdf | ||||||
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Title | Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II | ||||||
Components | Metal homeostasis factor ATX1 | ||||||
Keywords | METAL BINDING PROTEIN / Atx1 / metallochaperone / copper transfer / metal-binding domain / ferredoxin-like fold | ||||||
Function / homology | Function and homology information copper chaperone activity / copper ion transport / cellular response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Lee, M. / Maher, M.J. | ||||||
Citation | Journal: J. Inorg. Biochem. / Year: 2017 Title: The crystal structures of a copper-bound metallochaperone from Saccharomyces cerevisiae. Authors: Lee, M. / Cooray, N.D.G. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vdf.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vdf.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/5vdf ftp://data.pdbj.org/pub/pdb/validation_reports/vd/5vdf | HTTPS FTP |
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-Related structure data
Related structure data | 5vdeC 1cc8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 8232.650 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ATX1, YNL259C, N0840 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38636 #2: Chemical | ChemComp-CU1 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→58.09 Å / Num. obs: 45429 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.075 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2967 / CC1/2: 0.662 / Rpim(I) all: 0.669 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CC8 Resolution: 1.93→58.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.648 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.254 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→58.09 Å
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Refine LS restraints |
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